coerce: as("Slinky", "SummarizedExperiment")

In VanAndelInstitute/slinky: Putting the fun in LINCS L1000 data analysis

Description

Create SummarizedExperiment object from Slinky object. Data will be loaded from the GCTX file, combined with metadata from the info file, and wrapped in a SummarizedExperiment object. Note that this may take a long time for the entire data set from the L1000 project. For most use cases, a subset will be desired (e.g. as(sl[1:987,1:50], SummarizedExperiment). See the loadL1K method for a more flexible way to create a SummarizedExperiment object based on various query parameters.

See Also

loadL1K

Examples

# for build/demo only.  You MUST use your own key when using the slinky
# package.
user_key <- httr::content(httr::GET('https://api.clue.io/temp_api_key'),
                          as='parsed')$user_key
sl <- Slinky(user_key,
                 system.file('extdata', 'demo.gctx',
                      package='slinky'),
                 system.file('extdata', 'demo_inst_info.txt',
                     package = 'slinky'))
sumex <- as(sl[, 1:20], "SummarizedExperiment")

VanAndelInstitute/slinky documentation built on Aug. 20, 2021, 1:05 p.m.